[tdwg-content] Another example of non-overlapping concepts

Fri May 13 22:41:08 CEST 2011

Hi Nico,

Thanks for posting this.

I have something in the concept model to indicate the basis for the species
concept.

For now I have three types. An individual species concept can have a
combination of one, two or all three

In the RDF they look like this

<txn:speciesConceptBasedOn rdf:resource="
http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel"/>

The first is what I call the #ObjectiveSpeciesModel - this indicates that it
is a species concept because we say it is.

All the species concepts are at least an #ObjectiveSpeciesModel

*This is in part a way to handle things like the domestic cat which you want
to be seen as different from the African Wildcat.

There are also tags for

txn:PhylogeneticSpeciesModel
txn:BiologicalSpeciesModel

For now I don't have these other models set in the example data, but fields
are in the database and the code for that an editor could state the basis
for the model.

I can think of a couple of different ways to handle the issue of alternative
species concepts.

* Note that the identifications as proposed by DarwinCore don't seem to
indicate what kind of model the identifications were based on.
  So it is not clear to me if a straight DarwinCore data set would allow the
analysis above.

Instead of having multiple different statements like

*txn:occurrenceHasSpeciesConcept <> *in the record for each occurrence

one could use different predicates to link to different kinds of species
concepts.

*txn:occurrenceHasUniprotConcept* => <http://purl.uniprot.org/taxonomy/9696>

This would allow someone to query for the occurrences of <
http://purl.uniprot.org/taxonomy/9696>

That said, it is not clear to me what people mean by different
identifications.

Is the intent to have identifications with different homotypic synonyms to
be an identification of the same thing or not?

The way it works now in many data sets is that Felis concolor, Puma concolor
and Puma conncolor are treated as identifications of different things.

This is another way of saying* is the namestring the concept?*
*
*
My understanding of the eBird project is that it allows citizen scientists
to contribute their own observations. This creates a much larger data set
for analysis etc.

They have a created a curated list of species and a ~6 letter code for each.
This serves as a guide for observers on how to encode their observations.

I think their progress would be inhibited, the occurrence coding
inconsistant, and contributors frustrated, if they have a list that included
many overlapping species concepts.

Thanks again for you comments,

- Pete

On Fri, May 13, 2011 at 3:05 AM, Nico Franz <nico.franz at upr.edu> wrote:

>  Hello Pete (et al.):
>
>    For bird, Town Peterson at KU and colleagues have published these papers
> showing how alternative bird taxonomies affect the ranking of conservation
> priorities.
>
>
> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf
>
> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf
>
> http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf
>
>    Here's the abstract of the 1999 paper:
>
> Analysis of geographic concentrations of endemic taxa is often used to
> determine priorities for conservation
> action; nevertheless, assumptions inherent in the taxonomic authority list
> used as the basis for
> analysis are not always considered. We analyzed foci of avian endemism in
> Mexico under two alternate species
> concepts. Under the biological species concept, 101 bird species are
> endemic to Mexico and are concentrated
> in the mountains of the western and southern portions of the country. Under
> the phylogenetic species
> concept, however, total endemic species rises to 249, which are
> concentrated in the mountains and lowlands
> of western Mexico. Twenty-four narrow endemic biological species are
> concentrated on offshore islands, but
> 97 narrow endemic phylogenetic species show a concentration in the
> Transvolcanic Belt of the mainland and
> on several offshore islands. Our study demonstrates that conservation
> priorities based on concentrations of
> endemic taxa depend critically on the particular taxonomic authority
> employed and that biodiversity evaluations
> need to be developed in collaboration or consultation with practicing
> systematic specialists.
>
>    There was a debate recently on Taxacom that was started and subsequently
> neatly summarized by Fabian Haas. The topic was "let's summarize reasons why
> 'donors' seem to not fund taxonomy". One point from the summary was this:
>
> 3) Taxonomy is over-accurate for most applications
>
> Most (not all) decisions in e.g. modelling and conservation are done and
> can be done without complete knowledge of taxa. As it is, decisions for
> conservation areas are often based on flagship species (e.g. elephants), on
> taxa which have an excellent research background, e.g. birds (IBAs), on
> availability of land (e.g. land with a high Tsetse burden), importance as
> corridor and other factors, but never on a complete view on an all
> biodiversity in a specific area. Even if an inventory existed, it would be
> an illusion that we could collect data on ecological requirements and
> population dynamics for most of the species necessary for informed
> decisions. A complete inventory does not seem to provide an advantage for
> conservation.
>    I personally think there's some truth to that. I also think that, while
> it's understandable that an accurate representation of the (sometimes)
> fleetingness of taxonomic consensus it not a priority for applied ecological
> projects, if taxonomists themselves don't find better ways to document and
> link these alternatives perspectives, then it's not the best science we can
> do. That would be fine too if adopted outright as a pragmatic stance.
>
> Regards,
>
> Nico
>
>
>
> On 5/13/2011 1:08 AM, Peter DeVries wrote:
>
> I thought that I would also mention that in addition to The Plants List,
> the eBird project also uses on overlapping concepts in its bird list (it
> does have concepts for common hybrids)
>
>  What is clear to me is that you cannot create graphs like these if every
> observation can have X number of species (especially those that overlapping
> ) without any indication which is is the most appropriate one.
>
>  eBird Occurrence Maps Northern Cardinal
> http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal
>
>  NCBI is also similar.
>
>  Perhaps a member of the consensus committee can comment?
>
> -- Pete
>
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries at wisc.edu
> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
> Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>
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>
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-- 
------------------------------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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